Slowing down DNA translocation velocity using a LiCl salt gradient and nanofiber mesh

Yan, Han; Zhou, Daming; Shi, Baojun; Zhang, Ziyin; Tian, Haibing; Yu, Linfeng; Wang, Yunjiao; Guan, Xiyun; Wang, Zuobin; Wang, Deqiang

doi:10.1007/s00249-019-01350-x

Cited by 9 publications

(9 citation statements)

References 35 publications

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“…These methods focus either on nanopore material or deposition of an extra layer to retard DNA movement mechanically or electrostatically. 58,[63][64][65] Deposition of an agarose gel over a silicon-nitride nanopore or other 'guide structures' was shown to significantly reduce translocation speed, whereas functionalisation of the pore itself also produces similar results.…”

Section: B New Preparation Methods Suggests Single Molecule Accurate ...mentioning

confidence: 98%

Technologies for Size-Based Analysis of Circulating Cell-Free DNA: Limitations and Clinical Implementation

2022

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Prostate cancer is the second most common malignancy in men worldwide, and incidence is likely to rise in the next decade. The current screening options have limitations and have been shown to result in over-treatment of clinically insignificant disease. New biomarkers and technologies to detect them are therefore needed to better diagnose and stratify patients in primary care.Circulating cell-free DNA (ccfDNA) has gained interest as a potential minimally invasive biomarker, detectable in many bodily fluids (such as blood, urine, and cerebral spinal fluid) and reflecting the mutational landscape in tumours.More recently, the size distribution of ccfDNA fragments has also gained interest as a specific biomarker, where differences in size distribution have been observed between healthy volunteers and cancer patients, resulting in the new field of fragmentomics. Analysis of ccfDNA sizes provides avenues for alternative analytical technologies but commercial options are currently limited. Most focus on mutation detection and are subject to several biases that may affect size distribution.Here we discuss the available technologies and identify major issues and considerations that may affect their implementation as a clinically useful test based on ccfDNA size profiling.

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Section: B New Preparation Methods Suggests Single Molecule Accurate ...mentioning

confidence: 98%

Technologies for Size-Based Analysis of Circulating Cell-Free DNA: Limitations and Clinical Implementation

2022

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“…Slowing down of DNA translocation velocity using a LiCl salt gradient and nanofiber mesh was implemented to maintain the DNA molecule in the sensing time of nanopores. Compared to other alkali solutions, LiCl can extend the dwell time by 20 ms (five times longer than NaCl and KCl) for which it reaches 100 ms when the concentration increases and the nanofiber mesh further retards it by 162 to 185 ms [ 171 ]. Lowering the translocation speed of ssDNA by using 15-fold increases in LiCl salt concentration brings counter-ion binding and effective lowering of the overall charge of DNA, which in turn lessens the electrophoretic driving power of the system to slow down the translocation velocity.…”

Section: Advancement Of Nanopore Sequencing As the 4th-generation Seq...mentioning

confidence: 99%

Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing

et al. 2022

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Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor’s office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.

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“…Solid-state nanopores were fabricated by a method described elsewhere. 34 Briefly, we formed a 50 nm thick SiN x membrane on a SiN x -coated silicon wafer by deep wet etching of the silicon layer in potassium hydroxide solution at 80 °C. On the membrane, we spincoated an electron beam resist (ZEP520, Zeon) and baked at 180 °C.…”

Section: ■ Conclusionmentioning

confidence: 99%

“…Several approaches have been verified to face this challenge . Among the various strategies examined, such as active controls by means of adding external forces through light irradiation and gate voltages as well as passive methods via changing viscosity , and temperature of liquid, a salt gradient approach was reported to be useful for manipulating the translocation dynamics through the induced self-built electric field that serves not only to slow down the motions of objects such as DNA − and nanoparticles − but also to raise the capture rates in the conduit. − Meanwhile, the mechanism is predicted to become ineffective in pores of size much larger than the Debye length since it relies on ion-selective transport across the membrane to induce ion concentration polarization via the profound influence of surface charges on the nanopore wall. − Despite the fact that such condition is common in nanopore sensing of relatively large particles and molecules such as viruses and amyloids, along with the fact that various intriguing phenomena have been found in resistive pulse sensing using submicrometer channels such as pore shape-dependent ion blockage characteristics, ,, deformations of soft particles, − and concentration-polarization-induced ionic current enhancements, , little experimental efforts have been devoted so far to assess the feasibility of the salt gradient approach for controlling the translocation dynamics of non-DNA objects in the non-ion-selective channels.…”

Section: Introductionmentioning

confidence: 99%

Salt Gradient Control of Translocation Dynamics in a Solid-State Nanopore

et al. 2021

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Tuning capture rates and translocation time of analytes in solid-state nanopores are one of the major challenges for their use in detecting and analyzing individual nanoscale objects via ionic current measurements. Here, we report on the use of salt gradient for the fine control of capture-to-translocation dynamics in 300 nm sized SiN x nanopores. We demonstrated a decrease up to a factor of 3 in the electrophoretic speed of nanoparticles at the pore exit along with an over 3-fold increase in particle detection efficiency by subjecting a 5fold ion concentration difference across the dielectric membrane. The improvement in the sensor performance was elucidated to be a result of the salt-gradient-mediated electric field and electroosmotic flow asymmetry at nanochannel orifices. The present findings can be used to enhance nanopore sensing capability for detecting biomolecules such as amyloids and proteins.

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Slowing down DNA translocation velocity using a LiCl salt gradient and nanofiber mesh

Cited by 9 publications

References 35 publications

Technologies for Size-Based Analysis of Circulating Cell-Free DNA: Limitations and Clinical Implementation

Technologies for Size-Based Analysis of Circulating Cell-Free DNA: Limitations and Clinical Implementation

Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing

Salt Gradient Control of Translocation Dynamics in a Solid-State Nanopore

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